Re: [Freesurfer] freeview slow/choppy

Hi Octavian, You could try updating to the newest freeview version from the nightly development release. It is built on newer VTK and Qt libraries, so that might be the difference. Update instructions can be found here: https://surfer.nmr.mgh.harvard.edu/fswiki/UpdateFreeview Best Andrew

Re: [Freesurfer] freesurfer error in matlab

If I understand correctly, you're having trouble running freesurfer binaries from within matlab, right? Is freesurfer fully sourced in your MATLAB environment? I’m guessing this is an issue with your DYLD_LIBRARY_PATH not being set, but it's possible there are other issues going on. You should

[Freesurfer] Job opening: Full/Part-time medical imaging scientist: PWI/DWI/ASL/SWI

External Email - Use Caution Dear list members, Please check the attached job ad for a medical imaging scientist position at Atlanta, GA. We need experts for medical imaging analysis, especially for PWI, DWI/DTI, ASL or SWI. The position could be part-time and projected based.

Re: [Freesurfer] Question re: hippocampal/amygdala subfields

That is correct, Tegan! And welcome to FreeSurfer ;-) Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com From: on behalf of Tegan Hargreaves Reply-To: Freesurfer support list Date: Tuesday, February 11, 2020 at 14:55 To:

Re: [Freesurfer] Problem with registration (PetSurfer)

what command does it happen with? Please send the full terminal output from the command On 2/11/20 1:01 PM, Marina Fernández wrote: > > External Email - Use Caution > > Dear experts, I am following PetSurfer steps > (https://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer). Something was >

[Freesurfer] Flip left-right orientation command

External Email - Use Caution Dear Freesurfer experts, Which command should I use to flip the left-right orientation of a T1 image?. Actually my image is in PIR orientation, I used the following command mri_info --orientation '/home/rmn/Desktop/study/E03/3d/coanat_E03.nii' *PIR*

[Freesurfer] Question re: hippocampal/amygdala subfields

External Email - Use Caution Hi all, I am fairly new to FreeSurfer and am implanting the hippocampal/amygdala subfields script in our participants. As there are two versions of the hippocampal script (i.e., version 10 that is only hippocampus and version 21 which is both), I

[Freesurfer] (no subject)

External Email - Use Caution Hi Eugenio - Hope you are well. I am trying to extract the HSF from a group of processed brains. Previously I used the command: quantifyHippocampalSubfields.sh 195950 HSF_Cannabis Has this changed? If so what is the new command? Thanks, Alan --

[Freesurfer] questions about batch running longitudinal data using long_submit_jobs on cluste

Hi there, I am trying to run some longitudinal data using freesurfer long_submit_jobs command on cluster. I have double checked my directory and files setup according to freesurfer longitudinal preprocessing wiki:https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Scripts. And it seems there

[Freesurfer] Problem with registration (PetSurfer)

External Email - Use Caution Dear experts, I am following PetSurfer steps (https://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer). Something was wrong using mri_coreg function because when I checked the registration with tkregisterfv this error was shown in the terminal:

Re: [Freesurfer] Thickness group normalization

External Email - Use Caution I got the idea but faced an issue with mris_preproc, the command is: mris_preproc --target 0_1 --s avg_subject_91_noexpopts --hemi lh --meas thickness --out avg_91_to_lh.mgh where 0_1 is target patient to map thickness, from

[Freesurfer] recon-all -make all

External Email - Use Caution Dear Freesurfer experts, I ran recon-all on 100 subjects. Around 20 of them needed manual corrections of the pial surface on the brainmask.mgz. 1.) Can I run the command: "recon-all -make all- s " on all 100 subjects and it will only recon-all the